The bus tours are great for seeing a lot and some of the guides are fantastic with what they know.
I did all of them in one day on the main lines (Uptown inc Harlem, Downtown, Brooklyn and Night Tour).
http://www.citysightsny.com/category.php?id=-1
FAO Schwarz could be a big hit with the kids (massive toy store)...
http://www.fao.com/index.html
Proper diners are great for breakfast, we went here every morning and it was great for the traditional waffles and pancakes and such...
http://www.menupages.com/restaurants/the-red-f lame/
There is also Planet Hollywood to eat in Time Square...
http://www.planethollywood.com/restaurants_new York.htm
You could also see if anything is on at Madison Square Gardens. A baseball or icehockey game is also possible.
The Top of the Rock (Rockefeller Center) at night is a must, amazing view!
Empire State is one to do early as the queues can get a bit mad.
Weather is also a consideration as it may well be freezing and possibly heavy snow.
There's a Madame Tussauds.